I installed all my wads on the real nand.
Basically, I'd recommend you to install one or two at the time, and then use the Wii System Menu to move them to the SD card.
This way you free up space to install more wads.

I've got c.ca 150 wads istalled on the real nand and they all work flawlessly.
You just move them to the SD card and play them from there, then your only limit is the size of the SD card.

For at least some of those cases (notably about half of the N64 games), you need to use Waninkoko CIOSes, not d2x. I don't remember the exact bases and revisions, but USB Loader GX specifically allows for emulated NAND from some. You can just install a Waninkoko CIOS alongside your d2x and set USBLGX to use that IOS for your problem games.

For at least some of those cases (notably about half of the N64 games), you need to use Waninkoko CIOSes, not d2x. I don't remember the exact bases and revisions, but USB Loader GX specifically allows for emulated NAND from some. You can just install a Waninkoko CIOS alongside your d2x and set USBLGX to use that IOS for your problem games.

some games doesn't work at all (Castlevania for example) on EmuNAND with USBLoaderGX (it requires Sneek environement).
Install them on Real NAND and use the loader to list both Real and Emulated NAND.

If you want to install some games which require old/different cIOS on your EmuNAND, it's a bit more complicated.

The (Quick, not a details tutorial) steps are :
1 - the cIOS
install all needed cIOS (rev17, rev19 (base 38 I think), d2x (different version have different compatiblity) in different slots on your Wii. preferably in the 240-250 range.

2 - The Emulated NANDs
You have two choice:
2.1 - put your EmuNAND path on the root (all the folders on the root, not inside /nand/ folder)
or
2.2 - use two different EmuNAND path : one on the Root (to use with cIOS rev17/19), one in a subfolder (/nand/ to use with cIOS d2x)
Note: old cIOS require the NAND to be on the root of the first FAT32 partition of the 512Byte/sector drive. subfolder support was added in rev21, multi-partition in d2x v3, 4K sector in d2x v4.

3- The Titles
Install problematic games in the EmuNAND located on the Root
Optional : If you use the dual path (root + subfolder), then install the problematic game in both EmuNANDs.

4- The Settings
Go into the problematic game's Settings to set the cIOS to the slot where you installed the required cIOS version (if you installed rev19 in slot 240, set the N64 games to cIOS 240)
Optional : If you use the dual path choice (root + subfolder), then also set the problematic game's settings "Nand path" to the root.

Result :
The USBLoaderGX will list all channels found on the "default" emuNAND (/nand/), using the default cIOS (d2x):
it will also see the problematic games as they are installed on the default EmuNAND, but these problematic games have a different setting : IOS and path

1 - the cIOS
install all needed cIOS (rev17, rev19 (base 38 I think), d2x (different version have different compatiblity) in different slots on your Wii. preferably in the 240-250 range.

4- The Settings
Go into the problematic game's Settings to set the cIOS to the slot where you installed the required cIOS version (if you installed rev19 in slot 240, set the N64 games to cIOS 240)

I have these things installed so can i do the the step 4 with the settings. I dont know much of the cios.sd:\wad\1OS236.wadsd:\wad\Backup HBC - MAUI.wadsd:\wad\cIOS9-v6174-TED.wadsd:\wad\cIOS11-v6174-TED.wadsd:\wad\cIOS16-v257.wadsd:\wad\cIOS20-v6174-TED.wadsd:\wad\cIOS30-v6174-TED.wadsd:\wad\cIOS36-v3094-TEND.wadsd:\wad\cIOS50-v4889-TED.wadsd:\wad\cIOS60-v6174-TED.wadsd:\wad\cIOS70-v6174-TED.wadsd:\wad\cIOS80-v6174-TED.wadsd:\wad\cIOS90-v6174-TED.wadsd:\wad\cIOS202[60]-v5.1R.wadsd:\wad\cIOS222[38]-v4.wadsd:\wad\cIOS223[37-38]-v4.wadsd:\wad\cIOS224[57]-v5.1R.wadsd:\wad\cIOS245[37]-d2x-v8-final.wadsd:\wad\cIOS246[38]-d2x-v8-final.wadsd:\wad\cIOS247[53]-d2x-v8-final.wadsd:\wad\cIOS248[55]-d2x-v8-final.wadsd:\wad\cIOS249[56]-d2x-v8-final.wadsd:\wad\cIOS250[57]-d2x-v8-final.wadsd:\wad\cIOS251[58]-d2x-v8-final.wadsd:\wad\RVL-cMIOS-v65535(v10)_WiiGator_WiiPower_v0.2.wadsd:\wad\USB Loader GX-UNEO_Forwarder_4_0_AHBPROT.wadsd:\wad\IOS-Update\IOS12-64-v526.wadsd:\wad\IOS-Update\IOS13-64-v1032.wadsd:\wad\IOS-Update\IOS14-64-v1032.wadsd:\wad\IOS-Update\IOS15-64-v1032.wadsd:\wad\IOS-Update\IOS17-64-v1032.wadsd:\wad\IOS-Update\IOS21-64-v1039.wadsd:\wad\IOS-Update\IOS22-64-v1294.wadsd:\wad\IOS-Update\IOS28-64-v1807.wadsd:\wad\IOS-Update\IOS31-64-v3608.wadsd:\wad\IOS-Update\IOS33-64-v3608.wadsd:\wad\IOS-Update\IOS34-64-v3608.wadsd:\wad\IOS-Update\IOS35-64-v3608.wadsd:\wad\IOS-Update\IOS37-64-v5663.wadsd:\wad\IOS-Update\IOS38-64-v4124.wadsd:\wad\IOS-Update\IOS41-64-v3607.wadsd:\wad\IOS-Update\IOS43-64-v3607.wadsd:\wad\IOS-Update\IOS45-64-v3607.wadsd:\wad\IOS-Update\IOS46-64-v3607.wadsd:\wad\IOS-Update\IOS48-64-v4124.wadsd:\wad\IOS-Update\IOS53-64-v5663.wadsd:\wad\IOS-Update\IOS55-64-v5663.wadsd:\wad\IOS-Update\IOS56-64-v5662.wadsd:\wad\IOS-Update\IOS57-64-v5919.wadsd:\wad\IOS-Update\IOS58-64-v6176.wadsd:\wad\IOS-Update\IOS61-64-v5662.wadsd:\wad\shop channel v21\RVL-Shopping-v21.wadsd:\wad\shop channel v21\IOS62-64-6430.wad

use modmii to get the cIOS and select which slot they will be installed to.
Don't overwite useful content on your Wii, check what you have using Syscheck (look in my signature) to see all your used slots and what's installed in them.
once you decided on empty slots (for example 240 to 244), use modmii to download cIOS rev17 and tell modmii you want to install rev17 in slot 240.
it will create a .wad file that you need to install using a wad manager.

The wiiware will work only on real nand and then i can move to the sd card i suppose?
Is there a danger of bricking? Ill install via wad manager 1.7
I only want to play 2 n64 games so maybe i will pass and not install the cIOS rev17 and rev19

When I download Waninkoko CIOS using Download Pages or Advanced Download, it doesn't ask for a slot to install and I can't see any option to edit this.

EDIT: I found how to edit, but it is somewhat confusing, you have to know all the CIOS codes to mark them for download and edit, but on Advanced Download, the name of the CIOS doesn't appear like on Download Pages.